DADA2 - FileNotFoundError: [Errno 2] No such file or directory: ‘table-dada2.qza’

[slh277]

Thank you @thermokarst! I tried re running the DADA2 command after removing the mismatch. The command ran for around 60 hours but spit out the following error:

$ qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end-minus.qza --p-trim-left-f 0 --p-trunc-len-f 270 --p-trim-left-r 0 --p-trunc-len-r 270 --o-representative-sequences rep-seqs.qza --o-table table-dada2.qza
Traceback (most recent call last):
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/q2cli/commands.py", line 231, in __call__
    path = result.save(output)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/qiime2/sdk/result.py", line 140, in save
    self._archiver.save(filepath)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 340, in save
    self.CURRENT_ARCHIVE.save(self.path, filepath)
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 161, in save
    allowZip64=True) as zf:
  File "/Users/sm939/miniconda3/envs/qiime2-2017.11/lib/python3.5/zipfile.py", line 1009, in __init__
    self.fp = io.open(file, filemode)
FileNotFoundError: [Errno 2] No such file or directory: 'table-dada2.qza'

I’m not sure what happened, for it to have not found the table-dada2.qza because isn’t this command supposed to generate that table??

[thermokarst]

Hi @slh277! It looks like maybe you ran into this error - can you take a look at the workaround suggested there and see if that works for you? Sorry you lost your progress after so much time spent on it. Also, don’t forget to experiment with --p-n-threads - you can experience a pretty significant speed-up by tuning this parameter to something makes sense for the system you are running QIIME 2 on. Let us know how it goes - thanks!

The parent issue for this TMP bug can be found here.